Molecular Genetics & Genomic Medicine最新文献

Backgroud: To investigate the clinical features and genetic etiology of one child with Okur-Chung neurodevelopmental syndrome (OCNDS). The pathogenic variation spectrum of the CSNK2A1 gene and the phenotype spectrum of OCNDS were analyzed retrospectively.

Methods: A patient was selected from the endocrinology department of Dongying People's Hospital in July 2024. The genetic etiology of the phenotypic abnormality was identified by whole-exome sequencing (WES). All previously reported cases of OCNDS were retrieved from China National Knowledge Infrastructure (CNKI), Wanfang Data, PubMed, and the ClinVar database, and the phenotype and pathogenicity of the CSNK2A1 gene were retrospectively summarized. The differences in the mutation location and clinical phenotype of the CSNK2A1 gene were analyzed in combination with the literature on cell and molecular genetics.

Results: One variant (NM_001895.4: c.149A>G:p.Tyr50Cys) were de novo and previously reported within the CSNK2A1 gene and has been identified as a potential cause of OCNDS. The clinical data of 65 patients with OCNDS were retrospectively analyzed. The main clinical characteristics of OCNDS were developmental retardation of the nervous system, intellectual disability, facial deformity, language disorder, and other system abnormalities. This specific variant is located within the Glycine-Rich loop domain. There were significant differences in sleep disorders, autism spectrum disorders, short stature, and developmental delays.

Conclusion: This study diagnosed an OCNDS patient caused by a heterozygous mutation NM_001895.4: c.149A>G:p.Tyr50Cys in the CSNK2A1 gene through exome sequencing technology, further expanding the pathogenic variant spectrum of this gene. A systematic literature review and analysis was conducted to provide a foundation for the subsequent demonstration, which was based on the findings of the review. The demonstration revealed that variants in critical residues within the kinase domain disrupt the protein's spatial conformation and impair its function. This provides molecular evidence for genotype-phenotype correlation. These findings contribute to the advancement of knowledge in the field of OCNDS pathogenesis and provide a foundation for the development of genetic counselling and targeted therapeutic interventions.

Background: Noonan syndrome is a congenital genetic disorder characterized by distinctive craniofacial features, short stature, and congenital heart disease. Dysregulation of the RAS/mitogen-activated protein kinase (MAPK) pathway is a common molecular mechanism underlying the pathogenesis of these disorders. Germline mutations in RIT1 have also been identified in patients with Noonan syndrome. Patients with RIT1 mutations frequently exhibit cardiovascular abnormalities such as hypertrophic cardiomyopathy and lymphatic disorders. However, it remains unclear when cardiovascular abnormalities and lymphatic disorders develop and whether these disorders influence prognosis during the fetal period.

Methods: We investigated the cardiovascular and lymphatic phenotypes of Rit1^A57G/+ embryos. To elucidate that the activation of MEK/ERK is the involvement of cardiac abnormalities in Rit1^A57G/+ embryos, we administered a MEK1/2 inhibitor to Rit1^A57G/+ embryos and investigated the cardiovascular phenotypes.

Results: At E16.5, Rit1^A57G/+ embryos exhibited cardiac hypertrophy without cardiomyocyte hypertrophy and demonstrated progressive cell proliferation. Furthermore, Rit1^A57G/+ embryos exhibited pulmonary valve stenosis and lymphatic vessel expansion. Maternal intraperitoneal injection of PD0325901, a MEK1/2 inhibitor, prevented cardiac hypertrophy in Rit1^A57G/+ embryos.

Conclusions: Rit1 mutation causes cardiovascular and lymphatic abnormalities in the fetal period, and that the activation of MEK/ERK is the potential pathogenesis of cardiac hypertrophy.

Background: Hypochondroplasia (HCH) is a rare genetic skeletal dysplasia characterized by short stature, disproportionate limbs, and complications such as learning differences. Currently, no treatments are approved to address HCH-related short stature, which can adversely affect quality of life. This study aimed to explore diagnostic processes, care pathways, daily life impacts, and unmet needs in HCH.

Methods: Ninety-minute interviews were conducted with nine children and young adults and 25 caregivers who had physician-confirmed HCH. Participants discussed diagnostic journeys, treatment considerations, and day-to-day challenges. Following interviews, two 90-min focus groups among caregivers (n = 10) were conducted to explore themes emerging during interviews.

Results: We found that diagnostic pathways vary significantly, with signs of HCH identified in utero or during infancy or early childhood. Families described complex psychosocial burdens that include impacts on daily activities and emotional challenges due to height differences and disproportionate limb length. Additionally, many people with HCH have complications that go beyond short stature and include developmental delays, learning differences, and seizures. Families desire more support and resources related to HCH.

Conclusion: Future efforts should focus on holistic, patient-centered strategies to better support individuals with HCH and their families.

Background: Congenital long QT syndrome (LQTS) is an inherited arrhythmia characterized by QT prolongation and increased risk of ventricular arrhythmias. Type 2 LQTS (LQT2) results from mutations in the KCNH2 gene encoding the hERG potassium channel. With the widespread use of next-generation sequencing, many KCNH2 variants have been identified but remain classified as variants of uncertain significance (VUS), including p.L693P, requiring functional validation.

Methods: A proband with recurrent syncope and prolonged QTc underwent whole-exome and family-based Sanger sequencing, which detected a heterozygous KCNH2-L693P mutation. HEK293 cells were transiently transfected with wild-type (WT) and/or mutant hERG plasmids. Western blotting, immunofluorescence, and whole-cell patch clamp were performed to assess protein maturation, trafficking, and channel kinetics.

Results: Western blot showed reduced levels of the 155 kDa mature hERG and accumulation of the 135 kDa immature form, consistent with trafficking defects. Immunofluorescence confirmed endoplasmic reticulum (ER) retention. Electrophysiology revealed complete current loss in homozygotes and ~39% residual WT current in heterozygotes, indicating dominant-negative-like suppression. The mutation shifted steady-state inactivation and delayed recovery.

Conclusions: The KCNH2-L693P mutation impairs hERG maturation and function, supporting its reclassification from variants of uncertain significance (VUS) to pathogenic and providing evidence for improved clinical management.

Purpose: To evaluate the disease biomarker response of venglustat in patients with Fabry disease (FD), utilizing data from a single-arm phase 2 study of venglustat and a placebo-controlled phase 3 study of agalsidase beta through historical control and case-matched analyses.

Methods: Eleven venglustat-treated male patients with classic FD in the phase 2 study were matched with placebo- or agalsidase beta-treated patients from the phase 3 study based on propensity scores at baseline. Changes from baseline in plasma globotriaosylceramide (GL-3 or Gb3) concentrations were analyzed at approximately 6-36 months.

Results: Venglustat treatment resulted in greater significant reductions in plasma GL-3 concentrations at 6 months from baseline vs. placebo (mean difference -2.56 μg/mL, p < 0.001), and at 24 and 36 months from baseline vs. agalsidase beta (mean difference -1.8 μg/mL, p < 0.05 and -2.35 μg/mL, p < 0.01, respectively). GL-3 concentrations continued to decline with venglustat for up to 3 years without plateauing.

Conclusions: Venglustat showed significantly greater reductions in plasma GL-3 concentrations than placebo after 6 months and agalsidase beta after 24 and 36 months. These findings support the potential of long-term venglustat treatment to reduce GL-3 accumulation in patients with classic FD. Further studies are needed to confirm clinical benefit.

Objectives: Alkaptonuria (AKU) (MIM number 203500) or homogentisic acid oxidase deficiency is a metabolic autosomal recessive disorder caused by mutations in the homogentisate 1, 2-dioxygenase (HGD) (MIM number 607474) gene. The HGD is located on chromosome 3q13 with 14 exons, and encodes the homogentisate 1, 2-dioxygenase enzyme, which is composed of 445 amino acids. Although AKU was first described more than 120 years ago, we lack studies investigating its mutational spectrum in Iran.

Materials and results: This study aimed to investigate the spectrum of homogenetic gene mutations in patients diagnosed with Ochronosis Alkaptonuria in Ardabil, Iran. To achieve this, all individuals affected by this disease, totaling 23 individuals, whose affliction with Ochronosis Alkaptonuria had previously been definitively confirmed, were enrolled in the study. Sanger sequencing identified five unique variants in the HGD gene (NM_000187.4), all of which were homozygous variants. Two of the variants (c.113delA and c.342+5G>A) were novel and have not been reported in variant databases, including gnomAD, ClinVar, and HGMD. Other identified variants were c.175delA, c.334T>G, and c.680T>C, which have been previously reported in variant databases.

Conclusion: In this study, the mutational spectrum of alkaptonuric ochronosis was investigated in Iran. The HGD gene is a well-studied gene, and hundreds of variants responsible for alkaptonuria have been reported to date. However, we found two novel variants that have not been reported in previous studies.

Background: Multiple epiphyseal dysplasia (MED, OMIM #600969) is sometimes a mild skeletal dysplasia with diverse clinical findings, including early-onset osteoarthritis and short stature. Radiographic surveys can identify delayed epiphyseal ossification and cartilaginous changes. Due to genetic heterogeneity in MED, with dominant or recessive inheritance, molecular testing is essential for its diagnosis.

Methods: The clinical manifestations, the results of laboratory examinations, and genetic analysis of a 14-year-old Pakistani male with MED are reported.

Case presentation: Here we present a male patient with type-1 diabetes and hypothyroidism with bilateral knee effusions, right knee flexion contracture, and chronic arthralgias in his elbows and wrists. Given his symptomatology, a diagnosis of juvenile idiopathic arthritis (JIA) was initially suspected. Radiographs revealed sclerotic changes and fragments in the femoral and tibial epiphyses, suggesting destructive arthropathy. Genetic testing identified a COL9A3 variant (c.148-1G>C), as well as CTLA4 deficiency. The COL9A3 gene produces type IX collagen, and mutations in this gene can disrupt collagen folding or its interaction with other cartilage components. Complications include joint damage and early osteoarthritis, possibly requiring surgery.

Discussion: To date, only three COL9A3 splice-site mutations have been linked to MED. Our patient's splicing variant (c.148-1G>C) is novel and is likely causative, based on similar pathogenic mutations. Our patient presented with symptoms suggestive of JIA, but radiographic findings were inconsistent with this diagnosis. Genetic testing revealed a new pathogenic splicing variant in the COL9A3 gene, confirming MED.

Conclusion: This case highlights the importance of early molecular testing if radiographic sclerotic changes are seen in the epiphyses due to the clinical and genetic heterogeneity of MED.

Introduction: IMAGe syndrome, a rare disorder caused by maternally inherited CDKN1C pathogenic variants, is characterized by intrauterine growth retardation (IUGR), metaphyseal dysplasia, adrenal hypoplasia congenita, and genitourinary abnormalities. We report a novel intronic CDKN1C variant in a 5-year-old Iranian girl with IMAGe syndrome.

Materials and methods: Clinical evaluations showed severe IUGR (birth weight 1850 g), disproportionate short stature (height 88 cm, -4.4 Z score), metaphyseal dysplasia, adrenal insufficiency (ACTH 1110 pg/mL, low cortisol), and dysmorphic features (frontal bossing, low-set ears). Whole-exome sequencing (WES) was performed to identify causative genetic variants.

Results: WES revealed a heterozygous CDKN1C intronic variant, c.787+4A>T, absent from gnomAD, ExAC, and ClinVar. SpliceAI (score: 0.82) predicted disrupted splicing, potentially leading to a gain-of-function effect. The variant was consistently classified as a Variant of Uncertain Significance (VUS) according to ACMG/AMP 2015 guidelines with 2020 updates. No other pathogenic variants were identified in genes related to skeletal dysplasia, adrenal insufficiency, or growth retardation. Sanger sequencing confirmed maternal inheritance in the proband, her healthy mother, and grandfather, consistent with CDKN1C paternal imprinting.

Discussion: This case broadens the genetic spectrum of IMAGe syndrome by identifying the first reported intronic CDKN1C variant associated with this condition. WES is crucial for diagnosis, and RNA analysis is needed to confirm the variant's functional impact. Rapid diagnosis is essential for managing life-threatening adrenal insufficiency.

Background: The 22q11.2 deletion syndrome (22q11.2DS) is mostly caused by deletions of 3 and 1.5 Mb, referred to as typical deletions, although atypical deletions have also been reported. The commonest features are congenital heart disease, immunodeficiency, facial dysmorphism, and developmental delay. However, phenotypic variability is remarkable, and the underlying mechanisms remain poorly understood.

Objective: To determine copy number variations (CNVs) in the 22q11.2 region and their association with clinical manifestations in Mexican patients with suspected 22q11.2DS.

Methods: Fluorescence in situ Hybridization (FISH) and Multiplex Ligation-dependent Probe Amplification (MLPA) assays were performed in 80 patients with suspected 22q11.2DS. Clinical characterization was carried out according to the criteria used by the 22q11.2 Consortium.

Results: FISH detected deletions in 51%, while MLPA detected CNVs in 54%. Typical deletions were observed in 86% of patients, whereas atypical deletions were found in 14%, including CNVs involving single genes (TBX1, TOP3B, and PRODH). Three families were identified with the 3 Mb deletion and exhibited a heterogeneous phenotype that cannot be explained by the microdeletion alone.

Conclusion: 22q11.2DS is a complex disorder for which MLPA is recommended to detect atypical deletions in FISH-negative patients, and to define deletion size, breakpoints, and genes in FISH-positive ones.

Background: We identified a novel ABCD1 variant (c.773T>G, p.Leu258Arg, NM_000033.4) in a Chinese pedigree affected by X-linked adrenoleukodystrophy (X-ALD). This missense variant in exon 1 is predicted to be pathogenic and likely constitutes the genetic basis of the disease phenotype in this family.

Methods: ABCD1 gene sequencing was performed in the Chinese pedigree. The pathogenicity of identified variants was assessed using computational prediction tools. Subcellular localization studies were conducted, and very-long-chain fatty acid (VLCFA) levels were quantified in patient-derived samples.

Results: Sequencing analysis identified a hemizygous missense variant in the ABCD1 gene (c.773T>G; p.Leu258Arg). In silico pathogenicity prediction using SIFT and PolyPhen-2 algorithms classified the p.Leu258Arg substitution as deleterious. Functional characterization revealed that the p.Leu258Arg variant impairs the peroxisomal membrane localization of the ABCD1 protein. Consistent with the established role of ABCD1 in peroxisomal β-oxidation, individuals harboring this variant exhibited significantly elevated serum levels of VLCFA. Specifically, the C26:0/C22:0 ratio was elevated 2.8-fold compared to control values, confirming impaired VLCFA metabolism.

Conclusion: In accordance with the "Standards and Guidelines for the Interpretation of Sequence Variants" established by the American College of Medical Genetics and Genomics (ACMG), we assessed the pathogenicity of the novel ABCD1 gene variant c.773T>G. This variant meets the following ACMG evidence criteria: PM1 (located within a critical functional domain or mutational hotspot known to lack benign variation); PM2 (absent or observed at very low frequency in population databases e.g., gnomAD, EXAC, 1000 Genomes); PP3 (multiple in silico prediction tools consistently suggest a deleterious effect on the gene or gene product). Integrating this evidence (PM1 + PM2 + PP3), the variant is classified as likely pathogenic based on ACMG guidelines. Experimental data from this study further substantiate the pathogenicity of the c.773T>G variant located in exon 1 of the ABCD1 gene. This finding broadens the spectrum of known pathogenic mutations in ABCD1 associated with X-ALD and provides crucial information for the molecular diagnosis of affected patients.